When creating molecular presentations or videos, showing everything at once can overwhelm the viewer. Sometimes, revealing or concealing parts of the structure at specific moments helps focus attention and communicate more clearly. But how do you make atoms disappear gradually without changing their transparency or using complex scripting?
This is where the Conceal atoms animation in SAMSON, the integrative molecular design platform, becomes extremely useful. Instead of adjusting opacity, Conceal atoms allows you to make specific atoms and their connecting bonds vanish over time in a clean, progressive manner using visibility toggles. It’s ideal for guiding the viewer’s attention, emphasizing specific domains, or showing molecular mechanisms step-by-step.
Why progressive concealment matters
For molecular modelers and educators, conveying information visually is key. If you’re trying to explain interactions, active sites, or structural rearrangements, being able to phase out atoms between exact animation frames without distracting transitions offers better control over what is visible—and when. This makes your message clearer, whether you’re presenting to students, peers, or collaborations.
How it works in SAMSON
Using the Conceal atoms animation is straightforward:
- Select the atoms and bonds that you want to make disappear over time.
- Open the Animation panel in SAMSON’s Animator.
- Double-click on the Conceal atoms animation effect.
This animation is made of four keyframes:
- Keyframes 1 → 2: All targeted atoms and their bonds are visible.
- Keyframes 2 → 3: The atoms are gradually hidden following their order in the selection.
- Keyframes 3 → 4: All selected atoms and bonds are completely hidden.
The concealment isn’t random—it follows the ordering of your selection, giving you creative control. Want to hide atoms from the center outward? Simply select them in that order.
Customize the transition
You can modify how the animation progresses by adjusting the Easing curve. This controls the speed of disappearance (e.g., accelerating, decelerating, linear), which can help fine-tune the visual pacing of your molecular story.
Where it shines
Conceal atoms is especially useful in cases like:
- Removing ligands or subunits after discussing their role
- Presenting layered structures by hiding outer shells progressively
- Creating educational animations that simplify complex assemblies step-by-step
Here’s an example in action:
Examples to learn from
Ready to experiment with this technique? You can find working examples that use this animation in SAMSON Connect:
To learn more about how this works, visit the full documentation page: Conceal atoms documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.